Gene loci information

Transcript annotation

  • This transcript has been annotated as DNA-directed RNA polymerases I, II, and III subunit RPABC1.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g10870 g10870.t2 TSS g10870.t2 12374323 12374323
chr_1 g10870 g10870.t2 isoform g10870.t2 12374456 12375202
chr_1 g10870 g10870.t2 exon g10870.t2.exon1 12374456 12374512
chr_1 g10870 g10870.t2 cds g10870.t2.CDS1 12374460 12374512
chr_1 g10870 g10870.t2 exon g10870.t2.exon2 12374587 12374661
chr_1 g10870 g10870.t2 cds g10870.t2.CDS2 12374587 12374661
chr_1 g10870 g10870.t2 exon g10870.t2.exon3 12374716 12375202
chr_1 g10870 g10870.t2 cds g10870.t2.CDS3 12374716 12375202
chr_1 g10870 g10870.t2 TTS g10870.t2 12375288 12375288

Sequences

>g10870.t2 Gene=g10870 Length=619
ATGGATGACGAAGCAGAAACATATAAATTATGGAGAATTCGCAAAACAGTCATGCAGAGG
ATATTTAGTGACACAAGATGAATTGGACCAAACATTAGAACAATTTAAAGAGCAATTTGG
AGATAAACCAAGTGAAAAACGACCAGCGAGATCTGATTTGATTGTTTTAGTACATCATAA
TGATGATCCAACAGATCAAATGTTTGTCTTCTTTCCTGACGAATCAAAAATTGGTATTAA
ACTCATCAGAACTTATTGTCAGCGTATGCAAGAAGAAAATATTCATAGAGCTATTATGGT
TGTTCAAGGATCAATGTCTCCATCGGCAAAACAAGTTCTCGGTGAAATGGCTCCAAAATA
CATCATTGAACAATTTCTCGAGTCAGAATTGCTTATCAATATCACAGAACATGAATTGAT
TCCTGAACATGTTGTGATGACTCCAGAAGAGAAAGTTGAATTGCTTGCTCGCTACAAACT
CAAAGAGAACATGTTGATGAGAATTCAAGCTGGAGATCCTGTCGCACGGTACTTTGGATT
AAAAAGAGGACAAGTCGTAAAAATTATTCGACCATCTGAAACTGCTGGAAGATATATTTC
TTATCGACTTGTTTGCTAA

>g10870.t2 Gene=g10870 Length=204
MTKQKHINYGEFAKQSCRGYLVTQDELDQTLEQFKEQFGDKPSEKRPARSDLIVLVHHND
DPTDQMFVFFPDESKIGIKLIRTYCQRMQEENIHRAIMVVQGSMSPSAKQVLGEMAPKYI
IEQFLESELLINITEHELIPEHVVMTPEEKVELLARYKLKENMLMRIQAGDPVARYFGLK
RGQVVKIIRPSETAGRYISYRLVC

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g10870.t2 Gene3D G3DSA:3.40.1340.10 - 14 131 0.00000
8 g10870.t2 Gene3D G3DSA:3.90.940.20 - 132 204 0.00000
5 g10870.t2 Hamap MF_00025 DNA-directed RNA polymerase subunit H [rpoH]. 131 204 21.16204
3 g10870.t2 PANTHER PTHR10535:SF0 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 18 204 0.00000
4 g10870.t2 PANTHER PTHR10535 DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 18 204 0.00000
10 g10870.t2 PIRSF PIRSF000747 RPB5 15 204 0.00000
1 g10870.t2 Pfam PF03871 RNA polymerase Rpb5, N-terminal domain 17 88 0.00000
2 g10870.t2 Pfam PF01191 RNA polymerase Rpb5, C-terminal domain 131 203 0.00000
7 g10870.t2 SUPERFAMILY SSF53036 Eukaryotic RPB5 N-terminal domain 18 132 0.00000
6 g10870.t2 SUPERFAMILY SSF55287 RPB5-like RNA polymerase subunit 129 203 0.00000

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0003899 DNA-directed 5’-3’ RNA polymerase activity MF
GO:0003677 DNA binding MF
GO:0006351 transcription, DNA-templated BP

KEGG

Orthology

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed